If I understand your question correctly, Gostats and topGO in Bioconductor.
Also DAVID http://david.abcc.ncifcrf.gov/ is an easy to use web based tool.

Paul.

On Tue, Apr 17, 2012 at 10:45 PM, Ed Siefker <ebs15242@gmail.com> wrote:

> Are there tools available for differential gene set analysis?
>
> e.g., if I apply the same treatment to two different cell lines,
> and find gene sets that are enriched in each with respect
> to untreated, can I compare the lists of gene sets and
> find ones that are significantly enriched in one but not
> the other?
>
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>



-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com

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